Reference Data with CVMFS without Ansible
Have an understanding of what CVMFS is and how it works
Install and configure the CVMFS client on a linux machine and mount the Galaxy reference data repository
Configure your Galaxy to use these reference genomes and indicesTime estimation: 1 hourSupporting Materials:Last modification: Nov 21, 2023License: Tutorial Content is licensed under Creative Commons Attribution 4.0 International License. The GTN Framework is licensed under MITpurl PURL: https://gxy.io/GTN:T00004version Revision: 13
The CernVM-FS is a distributed filesystem perfectly designed for sharing readonly data across the globe. We use it in the Galaxy Project for sharing things that a lot of Galaxy servers need. Namely:
- Reference Data
- Genome sequences for hundreds of useful species.
- Indices for the genome sequences
- Various bioinformatic tool indices for the available genomes
- Tool containers
- Others too..
From the Cern website:
The CernVM File System provides a scalable, reliable and low-maintenance software distribution service. It was developed to assist High Energy Physics (HEP) collaborations to deploy software on the worldwide-distributed computing infrastructure used to run data processing applications. CernVM-FS is implemented as a POSIX read-only file system in user space (a FUSE module). Files and directories are hosted on standard web servers and mounted in the universal namespace /cvmfs.”
A slideshow presentation on this subject is available. More details are available on usegalaxy.org (Galaxy Main’s) reference data setup and CVMFS system.
This exercise describes a manual process to install and configure CVMFS and Galaxy’s access to CVMFS. For a tutorial that uses Ansible to perform these tasks, see the Reference Data with CVMFS tutorial.
CVMFS and Galaxy without Ansible
If you wish to perform the same thing that we’ve just done, but by building the ansible script manually, follow these instructions. Otherwise, you have already done everything below and do not need to re-do it.
We are going to setup a CVMFS mount to the Galaxy reference data repository on our machines. To do this we have to install and configure the CVMFS client and then mount the appropriate CVMFS repository using the publicly available keys.
Hands-on: Installing the CVMFS Client
On your remote machine, we need to first install the Cern software apt repo and then the CVMFS client and config utility:
sudo apt install lsb-release wget https://ecsft.cern.ch/dist/cvmfs/cvmfs-release/cvmfs-release-latest_all.deb sudo dpkg -i cvmfs-release-latest_all.deb rm -f cvmfs-release-latest_all.deb sudo apt-get update sudo apt install cvmfs cvmfs-config
Now we need to run the CVMFS setup script.
sudo cvmfs_config setup
The configuration is not complex for CVMFS:
Hands-on: Configuring CVMFS
/etc/cvmfs/default.localfile with the following contents:
CVMFS_REPOSITORIES="data.galaxyproject.org" CVMFS_HTTP_PROXY="DIRECT" CVMFS_QUOTA_LIMIT="500" CVMFS_CACHE_BASE="/srv/cvmfs/cache" CVMFS_USE_GEOAPI=yes
This tells CVMFS to mount the Galaxy reference data repository and use a specific location for the cache which is limited to 500MB in size and to use the instance’s geo-location to choose the best CVMFS repo server to connect to. You can use the
cvmfs_quota_limitrole variable to control this setting.
In production UseGalaxy.org.au uses 100GB, different sites have different needs and you can make your cache smaller depending on your usage. E.g. if your users only use one dataset from the reference data (e.g. just hg38) then perhaps you don’t need such a large cache.
/etc/cvmfs/domain.d/galaxyproject.org.conffile with the following contents:
This is a list of the available stratum 1 servers that have this repo.
/etc/cvmfs/keys/data.galaxyproject.org.pubfile with the following contents:
-----BEGIN PUBLIC KEY----- MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEA5LHQuKWzcX5iBbCGsXGt 6CRi9+a9cKZG4UlX/lJukEJ+3dSxVDWJs88PSdLk+E25494oU56hB8YeVq+W8AQE 3LWx2K2ruRjEAI2o8sRgs/IbafjZ7cBuERzqj3Tn5qUIBFoKUMWMSIiWTQe2Sfnj GzfDoswr5TTk7aH/FIXUjLnLGGCOzPtUC244IhHARzu86bWYxQJUw0/kZl5wVGcH maSgr39h1xPst0Vx1keJ95AH0wqxPbCcyBGtF1L6HQlLidmoIDqcCQpLsGJJEoOs NVNhhcb66OJHah5ppI1N3cZehdaKyr1XcF9eedwLFTvuiwTn6qMmttT/tHX7rcxT owIDAQAB -----END PUBLIC KEY-----
Make a directory for the cache files
sudo mkdir /srv/cvmfs
Testing it out
Probe the connection.
Hands-on: Testing it out
sudo cvmfs_config probe data.galaxyproject.orgQuestion
What does it output?
If this doesn’t return
OKthen you may need to restart autofs:
sudo systemctl restart autofs
Change directory into
/cvmfs/and list the files in that folderQuestion
What do you see?
You should see nothing, as CVMFS uses
autofsin order to mount paths only upon request.
Change directory into
cd /cvmfs/data.galaxyproject.org/ ls ls byhand ls managedQuestion
What do you see now?
.locfiles, genomes and indices. AutoFS only mounts the files when they’re accessed, so it appears like there is no folder there.
And just like that we all have access to all the reference genomes and associated tool indices thanks to the Galaxy Project, IDC, and Nate’s hard work!
If you are developing a new tool, and want to add a reference genome, we recommend you talk to us on Gitter. You can also look at one of the tools that uses reference data, and try and copy from that. If you’re developing the location files completely new, you need to write the data manager.
Look at the repository
Now to configure Galaxy to use the CVMFS references we have just installed, see the Ansible tutorial.